I think keeping Spider-Man 2099 separate from the Spider-Man that most people are familiar with would be the best idea instead of tying the two universes so close together in a film (similar to Shattered Dimensions if that's what they had in mind). The only thing they'd need to is just refer back to the original Spider-Man and how Miguel had gotten similar powers based off of him.

Trying out these different sagas would be the best thing to do I think instead of just rebooting Peter Parker's Spidey again and again.